What I would do is boot up in Linux and run a VM of BartPE with an AV integrated with the USB passed through to the VM. This way if the AV complains it can't delete something, shutdown the VM, mount the drive and delete it.
Why Linux? It will prevent you from getting infected, and Linux doesn't understand NTFS permissions so you can delete anything you want without the whinny Windows telling you don't have rights to it.
Unless of course you are talking about a Linux/Mac virus, which then it is a whole different ball game.
